Package: rMAT
Type: Package
Title: R implementation from MAT program to normalize and analyze
tiling arrays and ChIP-chip data.
Version: 3.22.0
Author: Charles Cheung and Arnaud Droit and Raphael Gottardo
Maintainer: Arnaud Droit <arnaud.droit@crchuq.ulaval.ca> and Raphael Gottardo <rgottard@fhcrc.org>
Description: This package is an R version of the package MAT and contains functions to parse and merge Affymetrix BPMAP and CEL tiling array files (using C++ based Fusion SDK and Bioconductor package affxparser), normalize tiling arrays using sequence specific models, detect enriched regions from ChIP-chip experiments. Note: users should have GSL and GenomeGraphs installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'. Snow Leopard users can take advantage of increase speed with Grand Central Dispatch!
Year: 2009.
License: Artistic-2.0
Depends: R (>= 2.9.0), BiocGenerics (>= 0.1.3), IRanges (>= 1.13.10), Biobase (>= 2.15.1), affxparser
Imports: stats, methods, BiocGenerics, IRanges, Biobase, affxparser, stats4
Suggests: GenomeGraphs, rtracklayer
biocViews: Microarray, Preprocessing
URL: http://www.rglab.org
NeedsCompilation: yes
Packaged: 2016-05-04 03:13:03 UTC; biocbuild
Package: Starr
Version: 1.28.0
Date: 2009-10-12
Title: Simple tiling array analysis of Affymetrix ChIP-chip data
Author: Benedikt Zacher, Johannes Soeding, Pei Fen Kuan, Matthias Siebert, Achim Tresch
Maintainer: Benedikt Zacher <zacher@lmb.uni-muenchen.de>
Depends: Ringo, affy, affxparser
Imports: pspline, MASS, zlibbioc
Description: Starr facilitates the analysis of ChIP-chip data, in particular that of Affymetrix tiling arrays. The package provides functions for data import, quality assessment, data visualization and exploration. Furthermore, it includes high-level analysis features like association of ChIP signals with annotated features, correlation analysis of ChIP signals and other genomic data (e.g. gene expression), peak-finding with the CMARRT algorithm and comparative display of multiple clusters of ChIP-profiles. It uses the basic Bioconductor classes ExpressionSet and probeAnno for maximum compatibility with other software on Bioconductor. All functions from Starr can be used to investigate preprocessed data from the Ringo package, and vice versa. An important novel tool is the the automated generation of correct, up-to-date microarray probe annotation (bpmap) files, which relies on an efficient mapping of short sequences (e.g. the probe sequences on a microarray) to an arbitrary genome.
License: Artistic-2.0
biocViews:
Microarray,OneChannel,DataImport,QualityControl,Preprocessing,ChIPchip
LazyLoad: yes
NeedsCompilation: yes
Packaged: 2016-05-04 03:16:03 UTC; biocbuild
providing 
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